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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1roz
Original Entry
Title:
Transferase
Compound:
Deoxyhypusine synthase
Mutant:
No
UniProt/Swiss-Prot:
P49366-DHYS_HUMAN
EC Class:
2.5.1.46
Other CSA Entries:
Overview of all sites for 1roz
Homologues of 1roz
Entries for UniProt/Swiss-Prot: P49366
Entries for EC: 2.5.1.46
Other Databases:
PDB entry: 1roz
PDBsum entry: 1roz
UniProt/Swiss-Prot: P49366
IntEnz entry: 2.5.1.46
Literature Report:
Introduction:
Deoxyhypusine is a highly rare posttranslational modification that occurs in eukaryotes where the it is vital for the formation of the initiation factor eIF5A. The enzyme carrying the reaction out is deoxyhypusine synthase which is able to transfer a butylamine moiety from spermidine to a lysine in eIF5A, using NAD as a cofactor. Since active eIF5A is required for tumour cell proliferation, design of inhibitors for this enzyme could prove useful in the treatment of certain cancers. The high specificity of the enzyme is also of interest, because the only incidence of this modification in eukaryotic proteins appears to be in this particular case.
Mechanism:
The enzymatic reaction proceeds in four steps. First, hydride transfer from spermidine to NAD with concomitant deprotonation by His 288 leads to the dehydration of spermidine to dehydrospermidine. The dehydrospermidine is thus activated to act as an electrophile; nucleophilic attack from lys 239 transfers the butylimine moiety to the enzyme forming an imine-enzyme intermediate, releasing diaminopropane. The lysine residue from eIF5A to be modified then attacks as a nucleophile, resulting in the formation of eIF5A imine intermediate and regenerating the catalytic lysine residue. Finally, the imine is converted to the butylamine moiety to form deoxyhypusine and NAD. Hydride transfer to and from NAD is assisted by Glu 157 which activates C4 of the NAD through electrostatic interactions.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
701 0
Substrate
Hydride transfer occurs from spermidine to NAD forming NADH and dehydrospermidine. Later in the reaction cycle the NADH transfers the hydride to the eIF5A-imine intermediate to form the deoxyhypusine product and regenerate the NAD.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10734052 Current protein Ligand is essential for catalysis
PubMed ID 15100216 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 137 137Sidechain
ElectrostaticCofactor
ElectrostaticSubstrate
Activates the NAD towards accepting a hydride ion in the first stage of the reaction through repulsion between the rozC4's pi electrons and the negative charge. Subsequently activates the eIF5A towards accepting a hydride ion through repulsion between the CN double bond and the negative charge.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15100216 Current protein Mutagenesis of residue
PubMed ID 15100216 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 288 288Sidechain
Acid/baseSubstrate
Accepts proton from spermidine to facilitate hydride transfer. Subsequently releases proton back to the modified lysine in eIF5A to allow hydride transfer from NADH to occur.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15100216 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15100216 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 329 329Sidechain
ElectrophileSubstrate
NucleophileSubstrate
ModifiedModified
Acts as a nucleophile to accept the butylimine moiety from dehydrospermidine, forming an enzyme-imine intermediate. This then acts as an electrophile for transfer of the butylimine moiety to eIF5A with the lysine residue in eIF5A to be modified acting as a nucleophile.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10734052 Current protein Residue is covalently bound to intermediate, based on non-structural data
References:
1
Deoxyhypusine synthase generates and uses bound NADH in a transient hydride transfer mechanism.
E. C. Wolff and J. Wolff and M. H. Park
J Biol Chem 275, (13) 9170-7, (2000).
10734052
2
A new crystal structure of deoxyhypusine synthase reveals the configuration of the active enzyme and of an enzyme.NAD.inhibitor ternary complex.
T. C. Umland and E. C. Wolff and M. H. Park and D. R. Davies
J Biol Chem 279, (27) 28697-705, (2004).
15100216
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